Package htsjdk.samtools

Class CRAMIterator

java.lang.Object
htsjdk.samtools.CRAMIterator
All Implemented Interfaces:
SAMRecordIterator, CloseableIterator<SAMRecord>, Closeable, AutoCloseable, Iterator<SAMRecord>
public class CRAMIterator extends Object implements SAMRecordIterator, Closeable

  • Constructor Details

  • Method Details

    • advanceToAlignmentInContainer

      public boolean advanceToAlignmentInContainer(int refIndex, int pos)
      Skip cached records until given alignment start position.
      Parameters:
      refIndex - reference sequence index
      pos - alignment start to skip to

    • hasNext

      public boolean hasNext()
      Specified by:
      hasNext in interface Iterator<SAMRecord>

    • next

      public SAMRecord next()
      Specified by:
      next in interface Iterator<SAMRecord>

    • remove

      public void remove()
      Specified by:
      remove in interface Iterator<SAMRecord>

    • close

      public void close()
      Description copied from interface: CloseableIterator
      Should be implemented to close/release any underlying resources.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface CloseableIterator<SAMRecord>

    • getFirstContainerOffset

      public long getFirstContainerOffset()

    • assertSorted

      public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder)
      Description copied from interface: SAMRecordIterator
      Establishes that records returned by this iterator are expected to be in the specified sort order. If this method has been called, then implementers must throw an IllegalStateException from next() when a record is read that violates the sort order. This method may be called multiple times over the course of an iteration, changing the expected sort, if desired -- from the time it is called, it validates whatever sort is set, or stops validating if it is set to null or SAMFileHeader.SortOrder.unsorted. If this method is not called, then no validation of the iterated records is done.
      Specified by:
      assertSorted in interface SAMRecordIterator
      Parameters:
      sortOrder - The order in which records are expected to be returned
      Returns:
      This SAMRecordIterator

    • getCramHeader

      public CramHeader getCramHeader()

    • getValidationStringency

      public ValidationStringency getValidationStringency()

    • setValidationStringency

      public void setValidationStringency(ValidationStringency validationStringency)

    • getFileSource

      public SamReader getFileSource()

    • setFileSource

      public void setFileSource(SamReader mReader)

    • getSAMFileHeader

      public SAMFileHeader getSAMFileHeader()